Friday, May 31, 2013

Why did some species of birds evolve flightlessness? According to Kyle Elliott from the University of Manitoba and his colleagues, sea birds probably traded flying for diving. Okay, that seems pretty obvious so far, until you ask why birds can't do both. In fact, there are species of birds that can both fly and dive, notably the murres and cormorants examined in this study. So why give up flight? The answer may be because of energy expenditure and efficiency.

We’re so used to the fact that penguins are flightless that it seems like the natural state for these birds. However, the ability to fly was an advantage not to be discarded lightly. After all, being able to fly would actually be quite handy for birds that migrate vast distances, not to mention for quick escapes from sharks and orcas. Unfortunately, the better adapted your body is to swimming and diving, in terms of biomechanics and energy costs, the less adapted it is for flying.

The researchers compared the flying and diving energy costs in murres and penguins, which dive using their wings to propel themselves, and in cormorants, which dive using their feet to propel themselves. Of the three groups, only penguins are flightless.

During flight, murres expended the most energy, far more than similarly sized birds, and more than cormorants. Remember, murres use their wings for both flying and swimming. During dives, penguins expended the least amount of energy, followed by murres and then cormorants.

Thick-billed Murres (Uria lomvia)

These data suggest that wings can be great for flying or swimming, but not both. Murres, which do use their wings for both flying and diving, are mediocre at both. Cormorants reserve their wings for flying and so expend less energy flying and more energy diving. Penguins, which have devoted their wing structure solely to swimming, expend the least amount of energy doing so. I guess the lesson here is that if you really want to do something well, you have to specialize.

Thursday, May 30, 2013

Let’s set the scene. A person who is not at the hospital suffers a cardiac arrest. A bystander with limited or no medical training initiates cardiopulmonary resuscitation (CPR). Traditionally, that CPR has included both rescue breathing (to keep the lungs ventilated and supplied with oxygen) and chest compressions (to maintain blood flow to the vital organs). However, in recent years, studies have suggested that it’s best to forego the rescue breathing and only do chest compressions.

This conclusion has come as a relief to potential CPR performers, both because rescue breathing can be tricky and because it obviates the need to attach one’s mouth to that of a stranger of unknown medical condition. Unfortunately, according to Aaron Orkin of the University of Toronto, it now looks like that verdict may have been premature. Rescue breathing may not be necessary in urban settings where the victim is likely to receive real medical attention fairly quickly, but it can be a lifesaver in situations where response teams are delayed.

Orkin conducted a literature search to find out how rescue breathing altered survival rates for adult cardiac arrest victims in various settings. The studies were conducted all over the world. He found that while rescue breathing did not improve outcomes in cases where the patient received professional medical care in under five minutes, some studies did show that CPR with rescue breathing was slightly better for patients who had to wait over fifteen minutes for medical attention.

So, what’s a well-meaning bystander to do?

First, I’m not a medical professional, so you should take my opinions for the inept conjectures they are. Got that?

Second, the sad truth is that very few people come back from being resuscitated unscathed. Fewer than a quarter of patients survive the event even when it happens in the hospital right in front of doctors. For people who have a cardiac arrest outside of a hospital, that figure is less than 10%. And that’s counting everyone who is successfully resuscitated. The percentage of people who subsequently leave the hospital neurologically intact is much lower. This means that despite anyone’s best efforts, it may not matter whether a CPR-performing bystander included rescue breathing.

One huge caveat: not everyone who stops breathing does so due to heart failure. This is particularly true of children, who are also more likely to benefit from rescue breathing. Plus, you never know if the victim in front of you would have been the one to beat the odds. Bottom line, bystanders should definitely perform CPR if they can. Whether or not to include rescue breathing may depend mainly on how competent and/or willing they are.

Orkin, A. (2013). Push hard, push fast, if you're downtown: A citation review of urban-centrism in American and European basic life support guidelines Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine, 21 (1) DOI: 10.1186/1757-7241-21-32.

Tuesday, May 28, 2013

Update 6/2013:The U.S. Supreme Court just ruled that DNA samples can be taken from people who are arrested but not yet convicted.

Do you think the government should have your DNA or that of your loved ones on file? What if the information could help identify missing persons or human remains? And who should have access to the data? Considering that 100 million people will probably be part of a DNA database by the year 2015, these are not trivial questions.

Currently, there are many circumstances in which a person’s DNA might find itself in a government database. Many countries routinely collect DNA from all military personnel. Petitioning refugees and immigrants might have their DNA compared to their alleged family sponsors. And of course, the DNA of criminals and victims is often collected.

There are also programs with databases set up to combat specific problems, like human trafficking. DNA-PROKIDS collects DNA in an effort to thwart the illegal transport and adoption of children out of their native countries.

For most people, providing DNA samples is strictly voluntary. It’s also important to note that at this time, DNA profiling is used only for the identification of individuals. Police and government departments cannot delve into our genomes for health or personal information. However, policies change and technology improves. Joyce Kim and Sara Katsanis from Duke University Medical Center suggest we get on the ball and figure out how we want to regulate DNA collection before it’s too late.

A few of their questions:

Should the DNA databases be held privately or publicly?

Who should have access to the data and under what circumstances?

What kind of information should agencies be allowed to glean from the data? In the not too distant future, it will be a simple matter to find out a person’s genetic risk for health or cognitive problems. We probably won’t want everyone to have that information.

What provisions are there for either opting out or expunging one’s DNA from the records?

What do you guys think?For more on this story, read Virginia Hughes' fascinating article at Only Human.Joyce Kim, & Sara H. Katsanis (2013). Brave New World of human-rights DNA collection Trends in Genetics.

Monday, May 27, 2013

I'm taking a day off from writing science posts. However, I always have new stuff on the Stochastic Scientist Facebook page. If you like cool pictures, videos or science news, click the link to the left

to head over and like the page.

On the other hand, if you want a Memorial Day post, may I suggest you head over to my other blog: Logical Outlook?

Friday, May 24, 2013

How much would it cost to provide every person on Earth with electricity and clean-combusting cooking fuels by the year 2030? According to a multinational team of researchers led by Shonali Pachauri of the International Institute for Applied Systems Analysis, Austria, about 75 billion U.S. dollars per year.

Currently, over 20% of the world’s population do not have electricity. You can imagine how much less productive a society is if it must cease most types of work or learning at sunset. The lack of clean cooking fuels is an even bigger problem. The time and energy spent collecting traditional fuels (wood or coal) drains local economies. Even worse, the smoke from these stoves is known to cause illness and premature death, particularly in children. A traditional outdoor cookstove - a chulla - in rural Tamil Nadufired, as you can see, by any readily available material, here branches pulled from the rapidly deforesting barren lands, some salvaged scrap wood, dried dung cakes and coconut shells.Credit: McKay Savage 8/30/2012

Because of these issues, the United Nations has set the ‘International Year of Sustainable Energy for All’ goal of achieving universal access to modern energy by the year 2030. Using 2005 as a base year, the researchers created models with different scenarios of public support in order to calculate what sorts of investment and policy changes would be required to get to that goal. For example, in some cases, the energy changes have to be achieved without changing existing polices, in others, western countries come together to offer low-cost financing and grants.

Not surprisingly, if the affluent parts of the world refuse to offer substantial assistance, the rest of world will not have electricity by 2030. In fact, without infrastructure assistance in the form of subsidized fuel prices, microloans and grants, there will be even more people without access to clean fuels in the future. On the other hand, an investment of about $75 billion per year could very well provide everyone on Earth with modern energy. Remember, that would be a global contribution, it wouldn't have to all come from one country.

Needless to say, this is an estimate. Even if the models are accurate, we can’t predict which if any policy changes are going to be implemented to push the U.N.’s agenda along.

By the way, contrary to first impression, giving more people access to modern energy should not increase carbon emissions. This is because petroleum products give off less carbon than wood or other traditional cooking fuels. Also, modern stoves and lighting apparatuses are more efficient than traditional cookstoves. And if newly built energy grids focus much more heavily on renewable resources like wind or solar, the gains will be that much greater.

Thursday, May 23, 2013

There are so many things I love about this story, not the least of which is that the senior author on the paper is named Hudson Freeze. Kudos to his parents. More importantly, this study exposes a hitherto unsuspected problem with genomic studies. Not all the cells within a person contain the same genes.

To be clear, it’s not the phenomenon of having cells of different genotype that’s novel. Scientists have known about the existence of genetic ‘mosaics’ for over eighty years. Occasionally when cells divide, DNA replication or chromosome division goes slightly awry and you end up with two daughter cells that are not genetically identical.

The drawing below illustrates mosaicism (don’t worry about the name of the specific gene or syndrome in the captions, they’re from a different article).

What is new is the realization that mosaicism may have to be taken into account when doing genomic studies. Case in point, three young children with glycoyslation disorders. Briefly, these kids have mutations that prevent their cells from attaching the right sugars in the right places to their proteins. Sugar placement is surprisingly critical for a whole host of functions, including cognitive ability.

Here’s the interesting part: only some of these kids’ cells contained the relevant mutation. This made it difficult to accurately diagnose them, because genetic studies came up negative or inconclusive. The scientists realized that they were dealing with mosaicism. That is, only a subset of the kids’ cells were defective.Going forward, Freeze and his colleagues suggest that researchers be cautious about how much credence they pay to whole genome studies. Those studies obviously involve only a tiny fraction of a person’s cells and could possibly be misleading.

By the way, this study dealt with ‘somatic mosaicism’. The children with this condition had originated from a single fertilized egg and some of their cells had subsequently mutated. This is a common enough occurrence that some researchers believe we may all be somatic mosaics. Under rare circumstances, two fertilized eggs will fuse into one embryo (the reverse of identical twinning) and the resulting baby will have some cells that are derived from each of those eggs.

Wednesday, May 22, 2013

Once again, it's time for the Best Illusion of the Year contest, sponsored by the Vision Sciences Society.The top prize went to this video, made by Jun Ono, Akiyasu Tomoeda and Kokichi Sugihara of Meiji University.This illusion concerns apparent rotation generated by pure translation. Square patterns consisting of four segments appear to rotate when they move straightly at a constant speed across the grid background. More surprisingly, the rotations in opposite directions can be generated by exactly the same square patterns. This illusion might be explained by well-known inchworm illusion; inchworm illusion arises at the four segments one after another resulting in the impression of rotation. This illusion is new in the sense that the rotation is generated by puretranslation.

Full disclosure, it took me a bit of staring to see all the rotation patterns. You can judge for yourself.I loved the second prize winner, by Arthur Shapiro and Alex Rose-Henig from American University, but unfortunately I could not embed it here. Check it out and be prepared to spend some time playing with it.Finally, here's one I liked by Guy Wallis and David Lloyd from the University of Queensland.You can see the other finalists here.

Tuesday, May 21, 2013

Mass can be explained in two ways: by the amount of force required to accelerate an object (inertial mass) and by that object’s attraction for other objects (gravitational mass). For ordinary matter, these two measurements are equal. What about for antimatter? While we can’t yet answer this question definitively, we now have the first observations of anti-atoms within a gravitational field.

Where ordinary hydrogen is composed of one electron and one proton, antihydrogen is composed of a positron (anti-electron) and an anti-proton. Note that even though protons and positrons both have positive charges, they do not occupy the same roles. Despite their opposite charges, it’s the protons and antiprotons that have the same positions within their respective atoms. The same is true of positrons and electrons. So anti-atoms are just like regular atoms except with opposite charges. Oh, and there’s the fact that when anti-atoms meet normal atoms the two annihilate each other.

Physicists working with CERN’s ALPHA, an international collaboration with the purpose of studying antimatter, have succeeded in producing and capturing antihydrogen. The anti-atoms are trapped within the ALPHA apparatus until the scientists are ready to release them. Within a few milliseconds of this release, the anti-hydrogens annihilate against the regular matter wall of the trap. The position at which this annihilation occurs can then be detected. From this, the researchers can determine any gravitational effects.

Early experiments show that the gravitational mass of antihydrogen is not more than 100 times that of its inertial mass. Remember, these two numbers are equal for regular hydrogen and could also be equal for anti-hydrogen. At this stage, these initial experiments are not much more than proof-of-concept tests. However, the physicists are confident that they will crack this puzzle in the coming years.

Monday, May 20, 2013

Huntington’s Disease (HD) is one of those rare diseases for which we know the exact genetic cause. If either of your parents bequeathed to you a huntingtin gene with extra CAG repeats, you will one day succumb to this terrible illness. This means that if you have a family history of HD, you can choose to have yourself tested and thus learn your inevitable fate, at least with regards to HD.

Graphic showing the excessive repetitions of the cytosine-adenine-guanine (CAG) nucleotide sequence in a gene from a Huntington's disease patient (bottom) compared to a gene from a person without the neurodegenerative disorder (top).Credit: National Institute of General Medical Sciences, National Institutes of Health

There is one more implication of being able to test for HD. It means that doctors can now follow the progression of an illness in people who are completely asymptomatic but who will one day have that disease. This kind of certainty is very unusual in medicine. Even with the best family histories, you can’t know for sure if someone will one day succumb to Alzeimer’s or cancer.

Sarah Tabrizi of the University College London and her colleagues, including TRACK-HD (a multinational prospective observational study of HD) investigators, chose to take advantage of this circumstance. They enrolled close to 400 volunteers who had the HD genetic marker but who were asymptomatic. The subjects were followed for thirty-six months. During that time, they were tested for cognitive and motor skills and had periodic brain scans to detect any loss of white or gray matter. Not surprisingly, the subjects showed steady declines in many of these areas. More importantly, the doctors could use the data to construct a sequence of expected failings.

At first glance, this may seem like the world’s most depressing clinical study. Actually, it still seems that way after multiple glances. However, it’s important to keep in mind that the better HD is understood, the more chance there is for a cure. These data could also help doctors learn how to postpone or ameliorate the worst of the symptoms. Barring that, knowing the way the disease progresses could at least give people a more accurate assessment of their futures.

Friday, May 17, 2013

John Cook from the University of Queensland and his colleagues have now put to rest the idea that there’s no consensus on global warming. Global warming is real, and it’s caused by humans. So say over 97% of peer-reviewed climate studies.

The researchers pored through nearly 12,000 published papers on climate science and separated them into ones that explicitly endorse anthropogenic (human-caused) global warming, those that explicitly reject that premise, and those that offer no position on the matter. Of the papers that expressed any judgment at all on global warming, 97.1% clearly stated that humans were the cause. When the authors of the papers were asked to rate their own positions on global warming, that number increased slightly to 97.2%.For perspective, Greg Laden points out that, among scientists, there's as much credence paid to the notion that humans are not causing global warming as there is to the existence of Big Foot.

The scientific community has spoken. Global warming is real and we caused it. It’s up to us to fix it if we can.

Cook discusses his results below.

Still not convinced? By all means, check the results for yourself. Study author Dana Nuccitelli suggests you visit Skeptical Science's Consensus Project where you can sign up to review abstracts and make up your own mind.

Thursday, May 16, 2013

How well do early reading and math ability correlate with success later in life? Better than you might think, according to Stuart Ritchie and Timothy Bates from the University of Edinburgh. They found that reading and math achievement at age seven predicted socioeconomic status (SES) thirty-five years later.

The study participants included over 18,000 children born the same week in 1958. In 1965, when the kids were seven years old, their parents filled out surveys to determine their childhood SES. The parents provided information on their type of job (professional, skilled or unskilled), whether the family rented or owned their home and how many rooms it contained.

Also at age seven, the children were rated for math and reading ability, both on standardized tests and by their teachers’ personal evaluations. At age eleven, the kids were given intelligence tests, and at age 16, they were asked about their motivation and perceived ability to do well in school.

Finally, at age 42, the participants were asked how much education they had ultimately completed and to provide their current SES by the same measures indicated above.

There was a definite correlation between both math and reading ability and SES at age 42. This was true even after accounting for childhood SES and intelligence. If achieving a high SES is your top priority, you'd better hope you were paying attention in second grade.

As usual, I have a few comments about this data. First, correlation is not causation, and Ritchie is the first to point this out. Second, even if the association between early academic skills and future earning potential turns out to be true, this doesn’t mean that there aren’t other paths to success. Finally, there’s nothing magical about age seven. Kids in Finland don’t even start formal education until that age, and they have the best educated students in the world. I wonder what the results would have been if reading and math skills at a later age were included. In other words, would reading proficiency at age 12 correlate more or less strongly with future SES than reading ability at age 7?

While I agree that proficiency in math and reading are extremely important, I hope this study won’t be used to further stigmatize students who are not doing well. If this news galvanizes schools to make a greater effort to help students who are struggling, that’s all to the good.Ritchie, S., & Bates, T. (2013). Enduring Links From Childhood Mathematics and Reading Achievement to Adult Socioeconomic Status Psychological Science DOI: 10.1177/0956797612466268.

Wednesday, May 15, 2013

By now, many of you know that rock star Canadian Space Agency astronaut Chris Hadfield has returned to Earth from the International Space Station (ISS). Why do I call him a rock star?

While he was up there, one of his jobs was to answers questions from the public, and he did a delightful job. Frankly, I never even thought about many of the issues he addresses.For example, have you been itching to know how astronauts brush their teeth in space? Besides telling us how astronauts shave, sleep or exercise, Hadfield also explained some of the experiments that were conducted on board the ISS. Here's an example with a bonus of spectacular solar wind footage.

Tuesday, May 14, 2013

We’re ten times as much bacteria as we are human, if you go by cell numbers. But we don’t all have the same mix of microbes coating us inside and out. Family members tend to share bacterial communities with each other. No surprise there, since people living in close contact tend to interact physically and to eat the same foods. What may surprise you is to know that the microbe similarities extend to pets.

Researchers led by Rob Knight and Se Jin Song of the University of Colorado, Boulder compared the microbiota in families consisting of heterosexual couples living with or without their biological children and with or without dogs. Fecal, oral and skin swabs were taken from all humans and dogs in the study. The bacterial makeup of the humans was more similar to that of their family members than to unrelated people. The microbiota of humans was also more similar to that of their own pets than to other people’s dogs. In addition, adults who owned dogs had a greater diversity of skin bacteria.

Here’s the interesting part. A couple shared more skin bacteria with each other if they lived with a dog. There was a much smaller effect if the couple had children. It seems that dogs are better at transferring bacteria around than kids.

What’s behind all this? The authors note that dogs tend to have a much greater variety of skin/fur bacteria than humans do. If the dogs were passing some of those microbes on to their people, that would significantly alter the composition of the humans’ skin biota, but in a way that affected all family members equally.

Monday, May 13, 2013

Pancreatic cancer is particularly deadly, mostly because it tends to metastasize before it can be detected. Fewer than 6% of patients are still alive five years after diagnosis. Needless to say, anything that could improve people’s odds would be welcome. To that end, scientists from the Albert Einstein College of Medicine came up with a novel treatment plan. They use radioactive Listeria to attack the tumor cells.

Usually associated with severe food poisoning,the bacteriaListeria monocytogenes(shown above) can also be used to infiltrate cells. The scientists had previously noted that a non-lethal, attenuated strain of the bacteria (Listeriaat) was quickly cleared from healthy cells but not from tumor cells. They therefore decided to use Listeriaat to deliver a radioactive punch directly to cancer cells.To test this technique, the researchers generated metastatic pancreatic tumors in mice. They infected the mice with Listeriaat and found that the bacteria accumulated only within tumor cells. Critically, the Listeriaat were found in metastases all over the body, not just at the site of the primary tumor. The scientists then used anti-Listeria antibodies to attach the radionuclide 188Rhenium (188Re) to the Listeriaat. 188Re was chosen for its short half-life (only 16.9 hours). Its attachment neither killed nor affected the infectivity of the bacteria, now called ‘radioactive Listeriaat’ (RL).When cancerous mice were infected with RL, the number of their metastases decreased by 90%. Primary tumors also shrank by 64% after infection with RL. Most of the radioactivity within the mice was found in their metastases. There was no damage to normal tissues.These data suggest that the bacteria are bringing their radioactive payloads directly to the cancerous cells. It is especially encouraging that the radioactivity is accumulating in and killing metastatic tumors throughout the body. These cells can be exceedingly difficult to identify, let alone remove or kill.While these results are highly promising, one mouse study doth not a treatment make. Writing in Nature, Monya Baker has a list of critiques about the study, including the possibility that the technique will result in excessive levels of radiation throughout the body. We’ll have to see if further studies support the commencement of human clinical trials.

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.